[COOT] how to set the refinement map
Hello, After what felt like a reasonable amount of poking about, I can't find how to set the refinement map (yes, I tried 'set-refinement-map') although I did find that guess-refinement-map returns a good guess but doesn't seem to stop the Oops! Must Select Map to fit to! box from bothering me. (It could at least open the map selection dialog like what happens when you do Validate Check/Delete waters without first specifying a map.) Seems a bit perverse to be able to determine I very likely want to refine against map 1, but not to actually set it for me. I am usually launching coot from a script-generated command, so my maps are always in the same order and I can reliably set the refinement map to imol #1, so I'd like to do that on startup. Is there any real danger in coot just going ahead with a guessed refinement map instead of the halting dialog? (Given the subsequent confirmation screen and the possibility to undo.) Or likely I am missing something everyone else has figured out? Thanks, Seth
Re: [COOT] how to set the refinement map
Thanks Paul, Actually I do have a map button. But I'd rather write something in a script somewhere once than click the button and confirm the click EVERY time I start the program! Hmmm, I had tried the (set-imol-refinement-map 1) in my .coot but obviously the problem was the map did not yet exist. So close! A monkey in the wrench... but it works beautifully if I put the (set-imol-refinement-map 1) into a coot_refinement_map.scm file and then my script adds the --script coot_refinement_map.scm option to the command line launching the program (at the end, I guess, to be sure the map is already loaded by then). A small thing, but it felt time to get it right! Much gratitude (especially after building up a few new proteins and feeling that tangible time savings from coot's nice tools and keyboard shortcuts!), Seth On Mon, May 10, 2010 at 3:23 PM, Paul Emsley paul.ems...@bioch.ox.ac.ukwrote: Seth Harris wrote: Hello, After what felt like a reasonable amount of poking about, I can't find how to set the refinement map (yes, I tried 'set-refinement-map') although I did find that guess-refinement-map returns a good guess but doesn't seem to stop the Oops! Must Select Map to fit to! box from bothering me. Wow. It now strikes me that this is a pain if you don't have a Map button - which I guess you don't. Which makes me think that you are using the gtk1 version. OK, time for that to die out. (It could at least open the map selection dialog like what happens when you do Validate Check/Delete waters without first specifying a map.) Seems a bit perverse to be able to determine I very likely want to refine against map 1, but not to actually set it for me. I am usually launching coot from a script-generated command, so my maps are always in the same order and I can reliably set the refinement map to imol #1, so I'd like to do that on startup. In that case, I would have thought that (set-imol-refinement-map nnn) would do the trick (nnn is 1, in this case presumably). (you can only do that if map number nnn exists at the time). Is there any real danger in coot just going ahead with a guessed refinement map instead of the halting dialog? (Given the subsequent confirmation screen and the possibility to undo.) Or likely I am missing something everyone else has figured out? Maybe most others are using gtk2 version. Paul.
Re: [COOT] how to set the refinement map
Seth Harris wrote: Actually I do have a map button. Hmm... I see. But I'd rather write something in a script somewhere once than click the button and confirm the click EVERY time I start the program! OK, I'm not understanding you then. If you start from fresh and you read in more than one map before refining anything, then of course Coot will not know which map to use. Understandable it seems to me. And typically one does not do that very often - certainly not every time. If you use the state script, the state script contains the setting for the refinement map. If you write your *own* script then you can easily set the refinement map as you read in your interesting mtz file: (set-imol-refinement-map (make-and-draw-map x.mtz 2FOFCWT PH2FOFCWT 0 0)) Hmmm, I had tried the (set-imol-refinement-map 1) in my .coot but obviously the problem was the map did not yet exist. indeed. So close! A monkey in the wrench... but it works beautifully if I put the (set-imol-refinement-map 1) into a coot_refinement_map.scm file and then my script adds the --script coot_refinement_map.scm option to the command line launching the program (at the end, I guess, to be sure the map is already loaded by then). That will do then? A small thing, but it felt time to get it right! It is not clear to me if you need to get it right or you have succeeded in getting it right... Paul.